By Kevin Davies
April 15, 2005 | With considerable help from Perlegen Sciences, the Mountain View, Calif., offshoot of Affymetrix, the International HapMap Consortium is ahead of schedule and plans to build a much more detailed map of human genomic variation than originally anticipated.
The news coincides with a major publication by Perlegen in Science, presenting genotype data on 1.6 million SNPs typed in 71 Americans of African, Asian, and European ancestry. This massive body of SNP data has been publicly deposited into the dbSNP database (Build 124).
The HapMap consortium had already reached its stated goal of charting 1 million SNP markers of human variation, based on analysis of 270 DNA samples from a spectrum of human populations, six months ahead of schedule. Now, with an additional $3.3 million in public/private funding, the consortium aims to build a Phase II map that is three times denser than the latest build, incorporating a further 4.6 million SNPs from public databases. The resulting map density will be increased from one marker every 1,800 bases to one every 600 bases. The additional $3.3 million comes from sources including the Wellcome Trust, Genome Canada/Genome Quebec, Bristol-Myers Squibb, and Pfizer.
"This will help us create a far more powerful HapMap than we ever imagined," says Francis Collins, director of the National Human Genome Research Institute. "The payoff will be a better understanding of the genetic risk factors underlying a wide range of diseases and conditions."
"We are excited by the opportunity to apply our technology to all publicly available SNPs," says Perlegen vice president of genomics Kelly Frazer. This effort is so important that Perlegen is willing to contribute some of its own resources to make this possible.
"The first phase of the HapMap Project has allowed scientists to make important analyses of the human genome that were not possible with only the human DNA sequence. Researchers around the globe can access the HapMap data through free public databases, such as the HapMap Data Coordination Center, the NIH-funded National Center for Biotechnology Information's dbSNP, and JSNP Database in Japan."
In March, Perlegen netted $74 million in a Series D private placement, which will "enable us to continue in-licensing and developing a valuable pipeline of late-stage drugs, exploiting Perlegen's ability to target the right drugs to the right patients," said Robert Middlebrook, Perlegen's chief corporate development officer.
Hinds, D.A. et al. "Whole-genome patterns of common DNA variation in three human populations." Science 307, 1072-9; 2005